They are cheaper
Anecdotal info says shipping with a regional priority box will be cheaper, even if bicoastal, assuming you are under a certain weight. Which brings us to:

They have weight limits
There are two box sizes (A and B). The A box can weigh up to 10 pounds, the B box 15.

The boxes are flimsier
I'm assuming because these boxes are meant to be used once and not internationally USPS is skimping on the cardboard quality. I haven't received my order yet but they're free and how bad can they really be?

You have to print postage at home
Someone said their post office had the boxes over my Express Mail but no one else has seen them in-store. The website says postage needs to be purchased on-line

It seems complicated and I don't have any boxes yet so I'm not in a rush to figure it out. I have an auction ending soon that will go standard priority mail so I'll report back on how much I could have saved if I'd used those boxes ;)